The goal of this WP is to provide a collection of best practices and indicators for research software and workflows. To do this, the WP will engage with the 15 ELIXIR Communities, which will also provide use cases for the best practices.
WP2 is linked with the services and infrastructure developed in WP3, which will capture Community input to steer development and drive adoption of best practices.
WP4, which is about capacity building and training, will ensure ensure expertise/content from WP2 is disseminated across ELIXIR Nodes. WP2 will also provide support for the industry and scientific outreach activities in WP5.
Objectives
| O2.1 | Building the technical toolkit for software best practices | Task 2.1 |
| O2.2 | Identifying efficiency indicators for research software and workflows | Task 2.2 |
| O2.3 | Assessment and dissemination of best practices through Community engagement | Task 2.3 |
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Tasks
Task 2.1 Building the technical toolkit for software best-practices
The objective of this task is to implement the technical toolkit by building a compendium of best practices for quality, sustainability, and impact of research software and workflows in life sciences.
These best-practices will be used towards the definition of high-level processes (e.g. efficiency benchmarking, workflow optimisation). The task will be centred on developing the best-practices through a dialogue with technical stakeholders from relevant Communities (cf. Task 2.3) and is tightly linked with WP3, shaping service requirements, and adopting their technical solutions.
The task will also address:
- How to credit and recognise scientists for research artefacts beyond publication.
- Software Management Plans (SMPs) for sustainable research software. Specific attention will be provided for ML software, promoting the adoption of the DOME-ML registry and preparing data for ML, as well as FAIR for ML.
- Reproducible workflows, benchmarking, and optimisation.
Leadership: Silvio Tosatto (University of Padua), John Hancock (University of Ljubljana), Fotis Psomopoulos (CERTH)
Task 2.2 Identifying efficiency indicators for research software and workflows
The objective of this task is to identify indicators for evaluating the efficiency, quality, environmental sustainability, and scientific impact of research software in life sciences.
This will provide a basis for measuring the performance and usefulness of research software and will help stakeholders to make decisions about the sustainable development and use of such software.
Activities of this Task include defining and implementing a set of indicators to assess the impact and usage of software, as well as the recognition received by its developers and users.
The metrics used for this purpose will be aligned with the best-practices compendium (cf. Task 2.1). In close collaboration with WP3 and the different communities (cf. Task 2.3), technical benchmarking will be carried out, including defining relevant performance and functional requirements and assessing software capabilities against them.Finally, the task aims to identify indicators for algorithmic and data effectiveness, for further implementation in WP3 (cf. Tasks 3.3 and 3.4). The identified indicators will contribute to the technical toolkit (see D2.2).
Leadership: Fotis Psomopoulos (CERTH), Salvador Capella-Gutierrez and Laura Portell-Silva (BSC), Silvio Tosatto (University of Padua), Karel Berka and Radka Svobodova (UOCHB), Zsuzsanna Dosztányi (HUN-REN Research Centre for Natural Sciences), Fran Borovecki (University of Zagreb School of Medicine), Nanjiang Shu (Uppsala University), Artemis Hatzigeorgiou (Hellenic Pasteur Institute), George Spyrou (Cyprus Institute of Neurology & Genetics), Dan Ben-Avraham (Weizmann Institute of Science).
Task 2.3 Adoption of best practices through Community engagement
This task will engage with existing and emerging ELIXIR Communities as well as communities linked to ELIXIR to:
- Discuss and obtain feedback on the best practices and indicators developed in Tasks 2.1 and 2.2 from ELIXIR Communities
- Develop use cases that illustrate and test the best practices and indicators in real-world software and workflow development
- Promulgate these examples of the best practice toolkit both within ELIXIR Nodes (WP4) and to wider communities outside of ELIXIR (WP5).
This task will engage ELIXIR Communities with the work of Tasks 2.1 and 2.2. To this end, the Task will create a Community Engagement Dashboard capturing key indicators for involvement.
It will organise online meetings and hackathons to engage people and to showcase its recommendations. Some of these meeting will include participants from industry.
Leadership: John Hancock, Brane Leskošek and Polonca Ferk (University of Ljubljana), Silvio Tosatto and Damiano Piovesan (University of Padua), Fotis Psomopoulos (CERTH), Zsuzsanna Dosztányi (HUN-REN Research Centre for Natural Sciences), Henning Hermjakob (EMBL-EBI), Mijke Jetten (Health-RI), Karel Berka and Radka Svobodova (UOCHB), Anne-Francoise Adam-Blondon (INRAE), Jose María Carazo (CNB-CSICS), Lucy Poveda (SIB), Fran Borovecki (University of Zagreb School of Medicine), Vasilis Promponas (University of Cyprus), Dan Ben-Avraham (Weizmann Institute of Science).
WP Leaders
